In vivo footprinting and ligation-mediated PCR (LMPCR) are well-established methods for the examination of the chromatin structure of eukaryotic genes. Here, we describe an improved method (pyrophosphorolysis activated polymerization LMPCR or PAP-LMPCR) that overcomes the shortfalls of previous methods by being capable of reading through sequences that up to now were refractory to this type of analysis. This includes dinucleotide repeat sequences or GC-rich regions. We also describe conditions capable of distinguishing between different alleles, thus enabling the simultaneous analysis of monoallelically expressed genes without having to employ interspecies hybrids.